Sentence examples for alignment algorithm implemented from inspiring English sources
To construct a phylogenetic tree of ZFA, we aligned ZFA repeat units using a progressive multiple sequence alignment algorithm implemented in ClustalW.
We then aligned the sequences in each cluster using the local alignment algorithm implemented in DIALIGN [ 29], followed by the refinement algorithm from MUSCLE [ 30].
The progressive alignment algorithm implemented in Mauve allows also building a phylogenetic tree based on analysis of genome rearrangements.
> -wrap-foot> The accuracy of the homology search for the different query sequences was estimated using the search results obtained by the Smith Waterman local alignment algorithm implemented in SSEARCH (Pearson, 1991) as the correct result.
To align the whole genome assemblies of D. melanogaster, D. simulans, D. yakuba and D. erecta, we used whole genome multiple alignment algorithm implemented in the VISTA Genome Pipeline (Brudno et al. in prep).
With only two closely related species in our set, we chose the Smith-Waterman [ 46] pairwise, gapped local alignment algorithm (implemented as BestFit in the Wisconsin Package Version 10.3, Accelrys Inc., San Diego, CA) to align their orthologous intergenic regions, using default parameters (match = 10.000; mismatch = -9.000; gap creation penalty = 50; gap extension penalty = 3).
The multiple alignment algorithms implemented in the following software were used to align the amino acid sequences: M-Coffee [15], T-coffee [4], and Muscle [16].
The alignment algorithm, as implemented on a modest workstation, is computationally efficient, allowing for large-scale structural comparisons.
This type of alignment algorithm is implemented in a program called Vista [ 84].
The custom alignment algorithm being implemented in Java does not achieve quite the same performance as natively running aligners like BWA.
To assemble mate pairs with overlapping sequence, a standard overlap alignment algorithm was implemented in the form of a perl script to assemble sequences.
